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Searched refs:bam_aux_get (Results 1 – 25 of 147) sorted by relevance

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/dports/biology/hisat2/hisat2-2.2.1/li_hla/
H A Dalignments.hpp195 if ( !bam_aux_get( b, "CC" ) || !bam_aux_get( b, "CP" ) ) in GetRepeatPosition()
202 std::string s( bam_aux2Z( bam_aux_get(b, "CC" ) ) ) ; in GetRepeatPosition()
204 pos = bam_aux2i( bam_aux_get( b, "CP" ) ) ;// Possible error for 64bit in GetRepeatPosition()
229 if ( bam_aux_get( b, "NH" ) ) in IsUnique()
231 if ( bam_aux2i( bam_aux_get( b, "NH" ) ) > 1 ) in IsUnique()
239 if ( bam_aux_get( b, f ) ) in GetFieldI()
241 return bam_aux2i( bam_aux_get( b, f ) ) ; in GetFieldI()
248 if ( bam_aux_get( b, f ) ) in GetFieldZ()
250 return bam_aux2Z( bam_aux_get( b, f ) ) ; in GetFieldZ()
260 if ( bam_aux_get( b, "XS" ) ) in GetStrand()
[all …]
/dports/biology/vt/vt-0.57721/lib/htslib/test/
H A Dsam.c61 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get()
140 if (bam_aux_get(aln,"XA")) in aux_fields1()
202 if ((p = bam_aux_get(aln, "Y2")) && bam_aux2i(p) != -2147483647) in aux_fields1()
205 if ((p = bam_aux_get(aln, "Y3")) && bam_aux2i(p) != -1) in aux_fields1()
208 if ((p = bam_aux_get(aln, "Y4")) && bam_aux2i(p) != 0) in aux_fields1()
211 if ((p = bam_aux_get(aln, "Y5")) && bam_aux2i(p) != 1) in aux_fields1()
214 if ((p = bam_aux_get(aln, "Y6")) && bam_aux2i(p) != 2147483647) in aux_fields1()
217 if ((p = bam_aux_get(aln, "Y7")) && bam_aux2i(p) != 2147483648LL) in aux_fields1()
220 if ((p = bam_aux_get(aln, "Y8")) && bam_aux2i(p) != 4294967295LL) in aux_fields1()
227 if ((p = bam_aux_get(aln, "N0")) && bam_aux2i(p) != ival) in aux_fields1()
[all …]
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/test/
H A Dsam.c61 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get()
140 if (bam_aux_get(aln,"XA")) in aux_fields1()
202 if ((p = bam_aux_get(aln, "Y2")) && bam_aux2i(p) != -2147483647) in aux_fields1()
205 if ((p = bam_aux_get(aln, "Y3")) && bam_aux2i(p) != -1) in aux_fields1()
208 if ((p = bam_aux_get(aln, "Y4")) && bam_aux2i(p) != 0) in aux_fields1()
211 if ((p = bam_aux_get(aln, "Y5")) && bam_aux2i(p) != 1) in aux_fields1()
214 if ((p = bam_aux_get(aln, "Y6")) && bam_aux2i(p) != 2147483647) in aux_fields1()
217 if ((p = bam_aux_get(aln, "Y7")) && bam_aux2i(p) != 2147483648LL) in aux_fields1()
220 if ((p = bam_aux_get(aln, "Y8")) && bam_aux2i(p) != 4294967295LL) in aux_fields1()
227 if ((p = bam_aux_get(aln, "N0")) && bam_aux2i(p) != ival) in aux_fields1()
[all …]
/dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/
H A Dbam_color.c14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_md.c89 uint8_t *old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core()
101 uint8_t *old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core()
121 uint8_t *q = bam_aux_get(b, "RG"); in bam_fillmd1_core()
198 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core()
199 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
/dports/biology/stringtie/stringtie-2.1.1/samtools-0.1.18/
H A Dbam_color.c14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_md.c89 uint8_t *old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core()
101 uint8_t *old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core()
121 uint8_t *q = bam_aux_get(b, "RG"); in bam_fillmd1_core()
198 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core()
199 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
/dports/biology/seqan1/seqan-1.3.1/lib/samtools/
H A Dbam_color.c14 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
37 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
88 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_md.c80 old_nm = bam_aux_get(b, "NM"); in bam_fillmd1_core()
90 old_md = bam_aux_get(b, "MD"); in bam_fillmd1_core()
174 if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq; in bam_prob_realn_core()
175 if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq; in bam_prob_realn_core()
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dbam_color.c42 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
71 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
129 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_color.c.pysam.c44 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
73 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
131 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_fastq.c636 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index()
638 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index()
645 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index()
647 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index()
707 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
713 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
804 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
H A Dbam_fastq.c.pysam.c638 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index()
640 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index()
647 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index()
649 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index()
709 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
715 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
806 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
H A Dbam_mate.c73 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar()
74 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar()
189 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc()
198 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc()
245 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
H A Dbam_mate.c.pysam.c75 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar()
76 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar()
191 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc()
200 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc()
247 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
H A Dbam_markdup.c338 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score()
383 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template()
500 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence()
967 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates()
1001 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag()
1002 || bam_aux_get(b, "XA")) { in optical_retag()
1073 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original()
1099 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original()
1517 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates()
1521 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
H A Dbam_markdup.c.pysam.c340 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score()
385 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template()
502 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence()
969 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates()
1003 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag()
1004 || bam_aux_get(b, "XA")) { in optical_retag()
1075 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original()
1101 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original()
1519 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates()
1523 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
/dports/biology/samtools/samtools-1.14/
H A Dbam_color.c42 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCSi()
71 uint8_t *c = bam_aux_get(b, "CQ"); in bam_aux_getCQi()
129 uint8_t *c = bam_aux_get(b, "CS"); in bam_aux_getCEi()
H A Dbam_fastq.c636 bc = (char *)bam_aux_get(b1, opts->barcode_tag); in output_index()
638 bc = (char *)bam_aux_get(b2, opts->barcode_tag); in output_index()
645 qt = (char *)bam_aux_get(b1, opts->quality_tag); in output_index()
647 qt = (char *)bam_aux_get(b2, opts->quality_tag); in output_index()
707 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
713 if ((tag = (char *)bam_aux_get(b[best[1]], in flush_rec()
804 if (state->use_oq && (oq = bam_aux_get(b[n],"OQ")) && *oq == 'Z') { in bam2fq_mainloop()
H A Dbam_mate.c73 if ((data = bam_aux_get(b1,"ct")) != NULL) bam_aux_del(b1, data); in bam_template_cigar()
74 if ((data = bam_aux_get(b2,"ct")) != NULL) bam_aux_del(b2, data); in bam_template_cigar()
189 if ((data = bam_aux_get(dest,"MQ")) != NULL) { in sync_mq_mc()
198 if ((data_mc = bam_aux_get(dest,"MC")) != NULL) { in sync_mq_mc()
245 if ((data_ms = bam_aux_get(dest, "ms")) != NULL) { in add_mate_score()
H A Dbam_markdup.c338 if ((data = bam_aux_get(b, "ms"))) { in get_mate_score()
383 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_template()
500 if ((data = bam_aux_get(bam, "MC"))) { in make_pair_key_sequence()
967 if (bam_aux_get(dup, "SA") || (dup->core.flag & BAM_FMUNMAP) || bam_aux_get(dup, "XA")) { in mark_duplicates()
1001 if (bam_aux_get(b, "SA") || (b->core.flag & BAM_FMUNMAP) in optical_retag()
1002 || bam_aux_get(b, "XA")) { in optical_retag()
1073 if ((data = bam_aux_get(current->b, "do")) != NULL) { in check_chain_against_original()
1099 if ((data = bam_aux_get(current->b, "dt"))) { in check_chain_against_original()
1517 if ((data = bam_aux_get(in_read->b, "dt")) != NULL) { in bam_mark_duplicates()
1521 if ((data = bam_aux_get(in_read->b, "do")) != NULL) { in bam_mark_duplicates()
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/test/
H A Dsam.c80 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get()
141 p = bam_aux_get(aln, target_id); in test_update_int()
155 p = bam_aux_get(aln, next_id); in test_update_int()
197 p = bam_aux_get(aln, target_id); in test_update_array()
222 p = bam_aux_get(aln, next_id); in test_update_array()
289 if (bam_aux_get(aln,"XA")) in aux_fields1()
399 p = bam_aux_get(aln, "N2"); in aux_fields1()
405 p = bam_aux_get(aln, "N3"); in aux_fields1()
422 p = bam_aux_get(aln, "F1"); in aux_fields1()
432 p = bam_aux_get(aln, "F2"); in aux_fields1()
[all …]
/dports/biology/htslib/htslib-1.14/test/
H A Dsam.c80 uint8_t *p = bam_aux_get(aln, tag); in check_bam_aux_get()
141 p = bam_aux_get(aln, target_id); in test_update_int()
155 p = bam_aux_get(aln, next_id); in test_update_int()
197 p = bam_aux_get(aln, target_id); in test_update_array()
222 p = bam_aux_get(aln, next_id); in test_update_array()
289 if (bam_aux_get(aln,"XA")) in aux_fields1()
399 p = bam_aux_get(aln, "N2"); in aux_fields1()
405 p = bam_aux_get(aln, "N3"); in aux_fields1()
422 p = bam_aux_get(aln, "F1"); in aux_fields1()
432 p = bam_aux_get(aln, "F2"); in aux_fields1()
[all …]
/dports/biology/star/STAR-2.7.9a/source/
H A DsignalFromBAM.cpp22 uint8_t* aNHp=bam_aux_get(bamA,"NH"); in signalFromBAM()
142 uint8_t* aNHp=bam_aux_get(bamA,"NH"); in signalFromBAM()
148 … aNH=bam_aux2i(bam_aux_get(bamA,"NH")); //write a safer function allowing for lacking NH tag in signalFromBAM()
/dports/biology/vt/vt-0.57721/
H A Daugmented_bam_record.cpp66 ((md_aux=bam_aux_get(s, "MD")) && (md = bam_aux2Z(md_aux))); in initialize()
380 (aux=bam_aux_get(s, "MD")) && (md = bam_aux2Z(aux)); in print()
414 (aux=bam_aux_get(s, "NM")) && (nm = bam_aux2i(aux)); in print()

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